Single-nucleus transcriptomic analysis of pediatric pancreas reveals cellular heterogeneity and early neoplasia signatures during chronic pancreatitis
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Background
Pediatric chronic pancreatitis (CP) carries an elevated lifetime risk of pancreatic ductal adenocarcinoma (PDAC), yet the cellular and molecular mechanisms driving disease progression and early neoplastic transformation remain undefined.
Methods
We performed single-nucleus RNA sequencing (snRNA-seq) on pancreatic tissue from 15 pediatric CP individuals and 6 healthy controls (HC). Findings were integrated with peripheral blood flow cytometry immunophenotyping of 8 CP and 7 HC individuals and validated by histopathological assessment.
Findings
We identified 15 distinct cell populations and profound cellular remodeling in CP, including a 46% reduction in acinar cells and emergence of inflammatory fibroblasts as the dominant stromal population. Acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN) populations bearing early PDAC-associated transcriptional signatures were detected in most CP samples. Cell-cell interaction analysis revealed that 68% of CP-specific ligand-receptor interactions converged on ADM and PanIN populations via ECM-integrin and inflammatory pathways. Peripheral blood flow cytometry demonstrated concordant systemic immune activation, including elevated monocyte CCR2 and CD80, increased CD69 on T cells, and upregulated RORγt in regulatory T cells.
Interpretation
This atlas defines the cellular landscape and intercellular signaling networks underlying pediatric CP, identifying inflammatory fibroblasts and early neoplastic cell states as central features. These findings provide a molecular foundation for understanding cancer risk in pediatric CP and provide a resource to prioritize studies into potential therapeutic targets and biomarkers.
Funding
This work was supported by the Network for Pancreatic Organ donors with Diabetes (nPOD) and The Leona M. & Harry B. Helmsley Charitable Trust.
Research in context
Evidence before this study
Chronic pancreatitis (CP) is a progressive inflammatory condition marked by irreversible structural alterations, fibrosis, and the deterioration of pancreatic function, leading to considerable morbidity and a diminished quality of life. Prior studies have characterized immune infiltration patterns and fibroblast heterogeneity in adult CP and pancreatic cancer using single-cell approaches, and spatial transcriptomics have been applied to adult pancreatic tissues. A single-nucleus atlas of the normal human pancreas from neonatal and adult donors provided a cellular reference framework. However, no study had applied single-cell or single-nucleus transcriptomics to pediatric CP tissue. The cellular composition, immune activation states, fibroblast diversity, and presence of early neoplastic signatures in the pediatric CP pancreas were entirely uncharacterized, leaving a critical gap in understanding disease mechanisms in this population with distinct genetic etiology and elevated lifetime cancer risk.
Added value of this study
We generated the first single-nucleus transcriptomic atlas of pediatric CP by profiling nuclei from pancreatic tissue of 15 children with CP and 6 healthy controls. We identified significantly distinct cell populations in CP compared to HC and uncovered marked cellular remodeling, including significant reduction in acinar cells, major immune cell expansion, and the emergence of inflammatory fibroblasts. Critically, we detected acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia populations bearing PDAC-associated transcriptional signatures in most CP samples, providing the first molecular evidence of early neoplastic changes in a pediatric context. Cell-cell interaction analysis revealed that inflammatory fibroblasts preferentially signal to precancerous populations via ECM-integrin and metabolic pathways. Complementary peripheral blood flow cytometry demonstrated concordant systemic immune activation, linking tissue-level inflammation to circulating immune dysregulation.
Implications of all the available evidence
Taken together, the available evidence establishes that pediatric CP is characterized by profound cellular remodeling, inflammatory fibroblast-driven signaling to precancerous cell populations, and early molecular features of neoplastic transformation that may precede histologically identifiable lesions by years. The detection of ADM and early PanIN signatures in children raises an important question about whether current cancer surveillance guidelines, which recommend screening from age 40 to 50 years in hereditary pancreatitis, should be reassessed for pediatric-onset disease. Circulating immune markers, including monocyte CCR2, CD80, and T-cell CD69, represent candidate biomarkers for disease monitoring. These findings may inform the design of host-directed therapies aimed at modulating immune-stromal interactions to attenuate fibrosis and reduce long-term cancer risk. The cellular programs identified here may also be relevant to other forms of pediatric inflammatory pancreatic diseases.
